bactopia-prune

Removes stale Bactopia environments that no longer match current module versions.

Usage

bactopia-prune [OPTIONS]

Required Options

Option	Type	Default	Description
--bactopia-path	STRING		Directory where Bactopia repository is stored

Prune Options

Option	Type	Default	Description
--envtype	CHOICE (conda, docker, singularity, all)	all	The type of environment to check for stale items
--wf	STRING		Only check environments for the given workflow (default: all workflows)
--condadir	STRING	/home/rpetit3/.bactopia/conda	Directory where Conda environments are stored (NXF_CONDA_CACHEDIR env variable takes precedence)
--registry	STRING	quay.io	Registry to match Docker containers against
--singularity_cache	STRING	/home/rpetit3/.bactopia/singularity	Directory where Singularity images are stored (NXF_SINGULARITY_CACHEDIR env variable takes precedence)
--singularity_pull_docker_container	BOOL	false	Use Docker-based naming for Singularity images
--execute	BOOL	false	Actually remove stale environments. Default is dry-run (report only)

Additional Options

Option	Type	Default	Description
--verbose	BOOL	false	Print debug related text
--silent	BOOL	false	Only critical errors will be printed
--version, -V	BOOL	false	Show the version and exit.